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This page was generated on 2023-10-20 09:38:04 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 977/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
idr2d 1.14.0  (landing page)
Konstantin Krismer
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/idr2d
git_branch: RELEASE_3_17
git_last_commit: 9bb309b
git_last_commit_date: 2023-04-25 11:12:16 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for idr2d on kjohnson2


To the developers/maintainers of the idr2d package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: idr2d
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:idr2d.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings idr2d_1.14.0.tar.gz
StartedAt: 2023-10-18 01:31:53 -0400 (Wed, 18 Oct 2023)
EndedAt: 2023-10-18 01:37:28 -0400 (Wed, 18 Oct 2023)
EllapsedTime: 334.7 seconds
RetCode: 0
Status:   OK  
CheckDir: idr2d.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:idr2d.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings idr2d_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/idr2d.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘idr2d/DESCRIPTION’ ... OK
* this is package ‘idr2d’ version ‘1.14.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘idr2d’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
estimate_idr         6.518  0.159  10.245
estimate_idr2d       6.358  0.155   9.946
draw_hic_contact_map 3.564  0.059   5.537
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

idr2d.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL idr2d
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘idr2d’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (idr2d)

Tests output

idr2d.Rcheck/tests/testthat.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(idr2d)
> 
> test_check("idr2d")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 132 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 132 ]
> 
> proc.time()
   user  system elapsed 
 57.038   1.826  92.360 

Example timings

idr2d.Rcheck/idr2d-Ex.timings

nameusersystemelapsed
calculate_midpoint_distance1d0.0010.0010.001
calculate_midpoint_distance2d0.0000.0010.002
calculate_relative_overlap1d0.0010.0000.001
calculate_relative_overlap2d0.0020.0010.002
determine_anchor_overlap0.3510.0060.554
draw_hic_contact_map3.5640.0595.537
draw_idr_distribution_histogram1.5450.0532.467
draw_rank_idr_scatterplot1.8370.0522.913
draw_value_idr_scatterplot1.4080.0822.273
establish_bijection0.2480.0060.384
establish_bijection1d0.2570.0060.388
establish_bijection2d1.5760.0312.435
establish_overlap1d0.1380.0040.212
establish_overlap2d0.3860.0080.618
estimate_idr 6.518 0.15910.245
estimate_idr1d1.2480.0481.993
estimate_idr2d6.3580.1559.946
estimate_idr2d_hic2.7580.0254.263
preprocess0.0140.0000.020
remove_nonstandard_chromosomes1d0.1800.0160.300
remove_nonstandard_chromosomes2d0.3830.0330.625